This analysis is based on the single-cell RNA-seq dataset published in:
Tu, J. et al. (2021). Single-Cell Transcriptomics of Human Nucleus Pulposus Cells: Understanding Cell Heterogeneity and Degeneration. Advanced Science, 8(23), 2103631. https://doi.org/10.1002/advs.202103631
From the plots generated: - UMAP/tSNE: Reveal 6 biologically interpretable NPC subtypes. - DotPlot: Confirms canonical marker expression in annotated subtypes. - Pseudotime: Suggests HT-CLNPs are early progenitors transitioning into mature states such as effector or fibroNPCs.
This analysis use dataset “GSE165722”.
QC Violin Plot
Global cell type identities are assigned using SingleR, referencing transcriptional profiles from datasets such as the Human Primary Cell Atlas. This method enables the identification of broad cell categories (e.g., MSCs, T cells) based on cross-tissue gene expression similarity.
UMAP Clusters
This approach evaluates the activation level of each NPC subtype signature at the single-cell level using AUCell. While umap_clusters_celltype.png displays general cell type classifications inferred from global references, umap_npc_subtypes_auc.png reveals functionally distinct NPC subtypes based on enrichment of tissue-specific marker genes.
UMAP Clusters
## p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
## 1 0 1.8229819 0.868 0.317 0 0 CYR61
## 2 0 1.2440728 0.977 0.431 0 0 DCN
## 3 0 1.8586392 0.877 0.345 0 0 CTGF
## 4 0 1.3793767 0.947 0.417 0 0 LUM
## 5 0 1.7458917 0.940 0.456 0 0 FN1
## 6 0 0.6984552 0.915 0.438 0 0 CLU
Top Marker DotPlot
Cell Type Distribution Barplot
Pseudotime trajectory of NPC populations
Cell-cell communication of NPC populations
.counts.tsv.gz and
.cellname.txt.gz pairs are expected in
data/GSE165722/extracted/filtered_feature_bc_matrix/
directories for each sample. ## 📊 Additional Static Results